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- PDB-7s3b: Crystal structure of intact U2AF65 RRM-region bound to AdML-G5 ol... -

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Basic information

Entry
Database: PDB / ID: 7s3b
TitleCrystal structure of intact U2AF65 RRM-region bound to AdML-G5 oligonucleotide
Components
  • DNA/RNA (5'-R(P*UP*UP*(UD)P*GP*U)-D(P*(BRU))-R(P*CP*C)-3')
  • Splicing factor U2AF 65 kDa subunit
KeywordsRNA BINDING PROTEIN/RNA/DNA / RNA SPLICING FACTOR / RNA RECOGNITION MOTIF / POLYPYRIMIDINE TRACT / RNA BINDING PROTEIN-RNA-DNA complex
Function / homology
Function and homology information


U2AF complex / poly-pyrimidine tract binding / pre-mRNA 3'-splice site binding / mRNA 3'-end processing / C2H2 zinc finger domain binding / commitment complex / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / U2-type prespliceosome / molecular function inhibitor activity ...U2AF complex / poly-pyrimidine tract binding / pre-mRNA 3'-splice site binding / mRNA 3'-end processing / C2H2 zinc finger domain binding / commitment complex / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA Polymerase II Transcription Termination / U2-type prespliceosome / molecular function inhibitor activity / Protein hydroxylation / negative regulation of mRNA splicing, via spliceosome / negative regulation of protein ubiquitination / mRNA Splicing - Major Pathway / positive regulation of RNA splicing / spliceosomal complex / mRNA processing / mRNA splicing, via spliceosome / nuclear speck / enzyme binding / RNA binding / nucleoplasm / nucleus
Similarity search - Function
U2 snRNP auxilliary factor, large subunit, splicing factor / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / DNA/RNA hybrid / Splicing factor U2AF 65 kDa subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.89 Å
AuthorsJenkins, J.L. / Henderson, S. / Kielkopf, C.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM070503-15 United States
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Pre-mRNA splicing factor U2AF2 recognizes distinct conformations of nucleotide variants at the center of the pre-mRNA splice site signal.
Authors: Glasser, E. / Maji, D. / Biancon, G. / Puthenpeedikakkal, A.M.K. / Cavender, C.E. / Tebaldi, T. / Jenkins, J.L. / Mathews, D.H. / Halene, S. / Kielkopf, C.L.
History
DepositionSep 5, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0Jun 29, 2022Group: Atomic model / Data collection / Polymer sequence / Category: atom_site / entity_poly / pdbx_nonpoly_scheme
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _entity_poly.type / _pdbx_nonpoly_scheme.auth_seq_num
Revision 2.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Splicing factor U2AF 65 kDa subunit
B: DNA/RNA (5'-R(P*UP*UP*(UD)P*GP*U)-D(P*(BRU))-R(P*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9384
Polymers24,7262
Non-polymers2122
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-5 kcal/mol
Surface area10200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.668, 57.839, 76.938
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Splicing factor U2AF 65 kDa subunit / U2 auxiliary factor 65 kDa subunit / hU2AF65 / U2 snRNP auxiliary factor large subunit


Mass: 22237.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: U2AF2, U2AF65 / Details (production host): PGEX-6P / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P26368
#2: DNA/RNA hybrid DNA/RNA (5'-R(P*UP*UP*(UD)P*GP*U)-D(P*(BRU))-R(P*CP*C)-3')


Mass: 2488.339 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 206 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38.2 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 0.24 M Na Malonate, 26% Peg 3350, n-dodecyl-N,N-dimethylamine-N-oxide (=LDAO)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 28, 2016
Details: Rh coated collimating mirrors, K-B focusing mirrors
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 1.89→38.47 Å / Num. obs: 29672 / % possible obs: 99.2 % / Redundancy: 6.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.062 / Net I/σ(I): 10.1
Reflection shellResolution: 1.89→1.93 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 908 / CC1/2: 0.922 / Rpim(I) all: 0.232 / % possible all: 89.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimless0.5.17data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.89→34.85 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.89 / Phase error: 18.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1998 1961 6.61 %
Rwork0.1733 27711 -
obs0.1751 29672 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 98.36 Å2 / Biso mean: 27.5767 Å2 / Biso min: 8.6 Å2
Refinement stepCycle: final / Resolution: 1.89→34.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1455 163 34 207 1859
Biso mean--42.57 32.39 -
Num. residues----203
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.89-1.940.25121370.21251686182385
1.94-1.990.2421460.19911990213699
1.99-2.050.2271260.19212023214999
2.05-2.120.25931200.18820052125100
2.12-2.190.2421440.176220242168100
2.19-2.280.19831420.176419942136100
2.28-2.380.19391290.172719942123100
2.38-2.510.24681560.175819922148100
2.51-2.670.20961510.169719972148100
2.67-2.870.19391450.172820062151100
2.87-3.160.19451240.168520182142100
3.16-3.620.20191590.157119932152100
3.62-4.550.14611410.148419922133100
4.56-34.850.19391410.193819972138100

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